Undergraduate Research


2016/2017 Research banner

Montana AireyAnalysis of δ13C and δ15N in Blood and Plasma of Seabirds Within the Gulf of Maine”

Alex Ascher “A test of alternative hypotheses for the traits that predict the number of species in three coral reef fish families”

Spencer Showalter “The abundance and toxicity of Pseudo-nitzschia on the U.S. West Coast”

Mollie YacanoAssessing the Role of Macroalgae in Estuarine Silicon Cycling”


Katrina Catalano “The role of endurance swimming in the active dispersal of the Caribbean coral reef fish, Elacatinus lori”

Victoria Hanley “Learning capabilities of Pagurus longicarpus through visual cues and feeding”

Maria Henning “Aquatic N2O and CH4 emissions associated with oyster guts and biofilms”

Ekaterina Rar “Stable carbon and nitrogen isotope analysis of the Great Shearwater”


Calder Atta “Divergence in feeding behavior of herbivorous fishes from flooded forests”

Margaret Bruce “The role of vision in recognition of individual dominance in the American lobster (Homarus americanus)”

Sarah Margolis “An analysis of soil chemistry in relation to the growth rates of Ammophila breviligulata, Uniola paniculata and Spartina patens in the coastal dune environment of Hog Island, Virginia”

Barbara Muesing “Spatial Analysis of Potential River Herring Habitat in the Charles River Watershed”

Paul Riley “Encrusting sponges and their ecological interactions with fishes and corals at Calabash Caye, Belize”

Spring 2014

Anya Battaglino and Margaret Bruce (Atema)

Response of Homarus americanus to mirror reflections with and without odor plumes This research intends to measure a lobster’s response to the visual stimulus of its own mirror image in the presence of varied olfactory stimuli, to determine if mirror reflections are generally perceived as conspecifics. We chose to use mirror reflections so the visual stimulus could be completely controlled and manipulated, as well as completely separated from all olfactory signals. The olfactory stimuli included a bathwater plume containing a conspecific’s odor, a seawater plume (containing the lobster’s own odor), and no plume. Prior to the experimental trials, aggressive behaviors were observed during lobster-versus-lobster fights. Using this data, an assay of measurable parameters for identifying aggression was established. In the mirror trials, individual lobsters were be observed for three minutes each. The observation tank contains a slide-in mirror piece with a hole 2 millimeters in diameter placed 8 centimeters from the bottom of the tank (approximately the height where lobsters’ olfactory organs are located). This hole was used to deliver the various odor plumes. The same experiment was then be repeated with a non-reflective surface, to further isolate the variable causing aggressive behavior. We hypothesized that our results would indicate that a lobster will respond more aggressively to its reflection in the presence of a conspecific odor than it would with the mirror and without the odor, or without the mirror and with the odor.

James Ferritto (Buston)

The Effect of Water Flow on Spawning Habitat Selection and Reproductive Success of the Sponge Dwelling Neon Goby, Elacatinus lori.

One of the main focuses of Ecology is to determine what factors affect the fecundity of an organism. Many elements affect an organism’s reproductive fitness, including, mate availability, predation, competition, disease, and habitat quality. In reef fish, the choice of spawning habitat has major consequences for an individual’s reproductive success. Yet, there is a gap in our knowledge of how adult fish identify appropriate spawning habitat.

I propose an investigation of the sensory cues used to select spawning habitat and subsequent effect of habitat choice on reproductive success in the neon goby Elacatinus lori. On the reef, E. lori is a facultative sponge dweller, and lives almost exclusively in association with the yellow tube sponge Aplysina fistularis (D’Aloia et al. 2011). Males defend a sponge tube as their territory, in which females visit to breed. Eggs are deposited on the inner wall of the sponge tube where they develop for approximately 7 days before hatching. During this time, the clutch is oxygenated and protected by the male, presumably with help from water flow through the sponge (Majoris personal observations). It has been demonstrated that male E. lori show a preference towards larger sponge tubes, however, the exact reason for this preference has not been demonstrated (Majoris et al. in prep). Larger sponges may have higher flow rates that could aid in the successful incubation of E. lori clutches. Thus the objective of the proposed project is to investigate the importance of flow rate cues on male habitat selection, reproductive success, and spawning frequency.

Spring 2013

Kirsten Krock (Murray)

The objective for this Undergraduate Research course is to analyze global warming in the Arctic and how this will affect U.S. Naval operations, research opportunities and global shipping.  The plan of the study will emphasize Department of the navy published policies and planning from 2009 and 2010. Part of the study will compare predictions and actions taken by the Navy for 2009-2012. The lsat phase of Navy planning is from 2013-2014 and an analysis will be conducted to recommend changes or an adjustment of the timeline. The rationale for this research is in line with the international significance of the impacts of global warming in the Arctic. Global warming specifically affecting this area of the world will not only affect the ecosystem by destruction of the habitat but will have large scale implications for how many countries conduct their travel for both commerce and military operations. I will be comparing plans and strategies outlined by the U.S. Navy to the very latest scientific understandings as articulated by the international scientific bodies such as the United Nation’s “Intergovernmental Panel on Climate Change (IPCC; www.ipcc.ch) reports. I will also take advantage of other US governmental resources, such as those of the US Arctic Research Commission (www.artic.gov) to frame my discussion.

Victoria Pinheiro (Murray)

A first-order groundtruthing of an ecosystem-based management model for the Stellwagen Bank National Marine Sanctuary. Research Proposal

Trevor Etheridge (Finnerty and Di Santo)

This research will examine the effects of hypoxia on the incubation time of little skate eggs (Raja erinacea). Research exposing several species of fish to hypoxic conditions has been previously explored, however no research has been done examining these effects on elasmobranches. This research will provide valuable insight regarding the response of this species to many issues presented by climate change. It is my current plan to expose the eggs to differing levels of dissolved oxygen during the last three months of their incubation. To accomplish this, I will set up a Shuttle box system, with which I can manage the water quality parameters of the system. Specifically, I plan on using the Shuttle box system to expose several groups of skate eggs to different oxygen levels, while exposing one group to standard dissolved oxygen levels as a control group.

Zachary Lepore (Finnerty)

The transcription factor NK-kB has been the subject of many studies because it is well conserved in many different organisms and is involved in the immune response. Additionally, this transcription factor exhibits some ontogenetic influence in certain organisms as well.  The model organism used in this research is the starlet sea anemone, Nematostella vectensis (Nv). Because of its involvement in immune response, understanding the complete network if NF-kB has implications in human disease development. A major part of the research will involve determining the target genes and downstream pathways of NF-kB. One topic involves the regeneration of cnidocytes, the phylum-specific cell type responsible for prey capture and defense. It has been shown that larval development of the body column cnidocyte requires NF-kB; however, future research will look into whether it is required for cnidocyte regeneration (and if the pathway is the same as during larval development) as well as if this pathway is found in other cnidarians.  Target genes will be identified through a variety of ways. One computation method will look for potential binding sites in the genomes of previously sequenced cnidarians. Common sequences found will then be experimentally tested with protein binding microarrays to determine the extent of the interaction between the NF-kB protein and its potential target genes.

Jillian Hayward (Lobel)

The objective for this Undergraduate Research course will be to conduct a comparative study of the two most prominent telemetry systems in marine mammal tagging. During the course, I will learn how to use both of the systems while comparing the pros and cons of each relative to different individual research needs. Each system will be applied on a stingray in the Lobel ichthyology tropical marine lab to track its movements in the tank and then use the data acquired to learn how telemetry data is downloaded and analyzed in MATLAB.  The final product of this course will be a scientific paper comparing the two systems, outline possible criteria for scientists to use as a method of choosing one system versus the other, supported using concrete data gathered in the stingray experiment.

Jillian Hayward (Finnerty)

This undergraduate research class will study the effect of a competing alga known to be found in close proximity with the northern star coral, Astrangia poculata. This experiment will compare growth, regeneration, and gene expression of Astrangia poculata with and without the presence of the competing alga.  Gene expresssion wil be dtermined using next generation RNA sequencing in the Finnerty lab.  Also, in order to produce a reference transcriptipon for Astrangia poculata, we will bioinformatically analyze the RNA sequence data collected in the “Marine Genomics” class.

Fall 2012

Blyss Buitrago (Kaufman)

Investigating the Grain Size Distribution of Fossilized Organisms in Sediment Across Reef, Seagrass Beds and Mangrove Habitats of Calabash Caye, Belize

Small scale interactions between reef communities are not highly research, especially taphonomy. This research looks at those fine scales details from a taphonomic approach, meaning we focused on the decaying, burial and preservation of marine organisms, tracing the path of these sediments from one habitat to another. Our study site was Calabash Caye on Turneffe Atoll in Belize, in the seagrass beds, mangroves and reefs. We obtained sediment cores in 2 locations of each habitat type, which were then analyzed for grain size distribution using ImageJ. From our data we were able to see the gradual decrease in size range as the sediment travelled from one habitat to another enduring erosion along the way. The seagrasses near reefs had the largest average grain size of Halimeda with a value of 3.94 mm, as they account for 25% of reef framework (Scoffin, 1992). In tropical areas over 90% of the beach sediment is composed of carbonate from reefs or calcareous algae and. In combination with our grain size analysis and obtained wind pattern information our research proved that our Calabash site was no exception.

Spring 2012

Elizabeth King (Kurtz)

Isotopic analysis is an important tool used in the natural sciences to draw inferences regarding age, composition, and sources for a number of processes. Perhaps the most popular form of isotopic analysis is the use of radioactive decay to measure the time elapse and ages of certain minerals, however there is another type of isotopic analysis that uses mass spectrometry to separate the different isotopes of an element based on the ratio of their masses. Mass spectrometry isotopic analysis is helpful when determining the different elemental composition in a sample, which in turn can be used to distinguish one geologic process from another. With respect to this project, I will be using the Thermal Ionization Mass Spectrometer to determine strontium isotope ratios for river samples from the Fly River system in New Guinea. The purpose of this experiment is to determine what chemical weathering processes contribute to the Fly River ecosystem. Strontium isotope ratios can be used as a proxy for continental chemical weathering and has further implications for CO2 drawdown in larger water bodies.

Erin McLean (Finnerty)

Determining areas of gene expression in Edwardsiella spp. sea anamones. The Finnerty lab works in the field of bioinformatics, studying the genome of Edwardsiella and Nematostella in order to understand the biodiversity at the molecular level.  My specific project would involve studying the genes of Edwardsiella and Nematostella to investigate how these genes regulate the development of the three layers of the blastula, eventually determining the body plan of the organism.

Joanna Grunin (Finnerty)

In Fall 2011, I completed a course in Marine Genomics (BI 550) as part of the Marine Semester. In Spring 2012, I intend to continue developing a bioinformatics project that I began during that class, namely a phylogenetic and structural analysis of two gene families (the Sox and Fox genes) in the lined sea anemone, Edwardsiella lineata.

Molly McCargar, Noelle Olsen (Finnerty)

A Comparative Study of Microbial Communities and Parasite Levels between Three Species of Surgeonfish. Research questions: How will microbial communities and parasite levels differ in Surgeonfish species that digest plant cells by mechanical breakdown of cellulose from species that chemically breakdown cellulose? Do differences in microbial communites correlate to phylogenetic distances between the fish species?

Erica Ross, Molly McCargar, Jess Molskness (Atema)

A Morphological Study on the Effect of Scales on External Taste Buds in Catfish. Research question: Does the presence of scales, or other keratinous growths, affect the abundance and distribution of external taste buds in catfish? It has been shown in previous studies that foraging behavior in catfish could be affected by the presence of keratinous appendages. It has also been shown that in other fish species scales restrict the number and density of peripheral taste buds. The purpose of this study is to investigate the changes in density and distribution of taste buds in catfish, and whether these changes are due to keratinous appendages.

Jillian Hayward, Zachary Rahaim (Atema)

Homarus americanus, the American lobster, has been known to engage in inner-species fights to determine dominance between individuals of the same sex.  Dominance in lobster populations is essential for the individuals to establish social hierarchies in which preference in mating shelters and successful mating with several females will be given to the most dominant (Atema et al. 1979; Karnofsky & Price 1989; Karnofsky et al. 1989a, 1989b; Cowan & Atema 1990).  It has been found that after engaging in a fight, lobsters can maintain memory of the fight for up to about one week by retaining sensory memory of the exchange of chemical information between individuals during the encounter (Karavanich & Atema 1998a; Moore & Bergman 2005).  It has been previously studied that the loser of the fight will recognize the dominant individual that it lost to and will display submissive behavior and a shorter fight duration.  An initial study of the memory of dominant lobsters indicates that they do not remember winning. In this study, we seek to further explore the sensory memory of the dominant individual by inducing a second fight against the same losing individual and observing and analyzing the behavior of the dominant lobster with respect to increased aggression levels and shorter fight duration. Lobster MMA trailer

Brendan Laing and Sarah Guitart (Kaufman and Gopal)

Seabirds are highly migratory and mobile members of any marine ecosystem. They serve as key indicators of local biomass and ecosystem health, as well as changing environmental conditions (Baird 1990). Seabird species exhibit strong responses to the ecosystem around them; Baird (1990) shows that a depletion of fish stock, leading to reduced prey availability, causes a reduction of reproductive success by up to 90%. Additionally, in areas with large fishing industries, seabirds often experience mortality due to by-catch (Soczek 2006). The relationship that pelagic birds have to their environment has not been perfectly quantified, and is just one component in an incredibly complex system (Peron et al. 2010).  Therefore, in order to fully utilize seabirds as habitat indicators, and to more effectively conserve these long-lived species (many of which are protected by law), more knowledge is needed about their distribution and behavior. This project aims to quantify the density distribution of seabirds in the northern part of Stellwagen Bank National Marine Sanctuary (SBNMS) using a thirty year, observational data set collected by the Whale Center of New England.   This work will be integrated with the recently launched Stellwagen Bank seabird survey conducted by the Stellwagen Bank National Marine Sanctuary and Mass Audubon, and to earlier data sets collected for the entire Sanctuary in the mid-1990’s.  The focus of this work is on the nature and determinants of dense seabird aggregations on Stellwagen Bank.

Fall 2011

Mary Katherine Rogener (Fulweiler)

The objective of this research course is to design a larger project that will go on to next semester and possibly next summer. The project will consist of looking at iron and manganese cycles and how these cycles influence the nitrogen cycle in coastal marine systems.

Hally Stone (Anderson)

Seasonal to Interannual Variations in the North Subsurface Countercurrent of the Equatorial Pacific Since their discovery over 30 years ago, little research has been done on the Pacific Subsurface Countercurrents, also known as the Tsuchiya Jets.  Although their dynamics, as well as their importance to local and global circulations, are beginning to be understood, very little work has gone into characterizing and understanding their variability and its sources. The purpose of this project is to study and characterize the seasonal and interannual variability of the North Subsurface Countercurrent with the use of a new ocean reanalysis.